Table 3.
Top networks queried by DAVID gene ontology annotation of genes uniquely misregulated in PCK or in FHH.Pkhd1 kidneys
| ID | Term | Count | % | P Value |
|---|---|---|---|---|
| A: PCK misregulated biological processes | ||||
| GO:0009611 | response to wounding | 26 | 7.28 | 4.27E-07 |
| GO:0003013 | circulatory system process | 14 | 3.92 | 7.26E-06 |
| GO:0008015 | blood circulation | 14 | 3.92 | 7.26E-06 |
| GO:0016042 | lipid catabolic process | 13 | 3.64 | 8.40E-06 |
| GO:0055114 | oxidation reduction | 29 | 8.12 | 1.22E-05 |
| GO:0006954 | inflammatory response | 16 | 4.48 | 1.53E-05 |
| GO:0016064 | immunoglobulin mediated immune response | 8 | 2.24 | 2.95E-05 |
| GO:0019724 | B cell mediated immunity | 8 | 2.24 | 3.87E-05 |
| GO:0002526 | acute inflammatory response | 10 | 2.80 | 4.83E-05 |
| GO:0006775 | fat-soluble vitamin metabolic process | 7 | 1.96 | 5.10E-05 |
| GO:0006952 | defense response | 21 | 5.88 | 6.76E-05 |
| GO:0008202 | steroid metabolic process | 13 | 3.64 | 8.02E-05 |
| GO:0019884 | antigen processing and presentation of exogenous antigen | 6 | 1.68 | 8.90E-05 |
| GO:0002495 | antigen processing and presentation of peptide antigen via MHC class II | 5 | 1.40 | 1.06E-04 |
| GO:0019886 | antigen processing and presentation of exogenous peptide antigen via MHC class II | 5 | 1.40 | 1.06E-04 |
| GO:0006955 | immune response | 21 | 5.88 | 1.11E-04 |
| GO:0002449 | lymphocyte mediated immunity | 8 | 2.24 | 1.42E-04 |
| GO:0002504 | antigen processing and presentation of peptide or polysaccharide antigen via MHC class II | 5 | 1.40 | 1.87E-04 |
| GO:0006873 | cellular ion homeostasis | 19 | 5.32 | 2.26E-04 |
| GO:0002460 | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 8 | 2.24 | 2.34E-04 |
| GO:0002250 | adaptive immune response | 8 | 2.24 | 2.34E-04 |
| GO:0055082 | cellular chemical homeostasis | 19 | 5.32 | 2.67E-04 |
| GO:0030168 | platelet activation | 5 | 1.40 | 4.70E-04 |
| GO:0002478 | antigen processing and presentation of exogenous peptide antigen | 5 | 1.40 | 4.70E-04 |
| GO:0002443 | leukocyte mediated immunity | 8 | 2.24 | 5.16E-04 |
| GO:0006766 | vitamin metabolic process | 8 | 2.24 | 6.06E-04 |
| GO:0050801 | ion homeostasis | 19 | 5.32 | 6.10E-04 |
| GO:0048002 | antigen processing and presentation of peptide antigen | 6 | 1.68 | 7.79E-04 |
| GO:0006631 | fatty acid metabolic process | 12 | 3.36 | 8.73E-04 |
| GO:0019725 | cellular homeostasis | 20 | 5.60 | 9.49E-04 |
| GO:0019882 | antigen processing and presentation | 8 | 2.24 | 9.51E-04 |
| GO:0048878 | chemical homeostasis | 21 | 5.88 | 0.001 |
| GO:0050778 | positive regulation of immune response | 10 | 2.80 | 0.001 |
| GO:0050817 | coagulation | 7 | 1.96 | 0.001 |
| GO:0007596 | blood coagulation | 7 | 1.96 | 0.001 |
| GO:0002684 | positive regulation of immune system process | 13 | 3.64 | 0.002 |
| GO:0007599 | hemostasis | 7 | 1.96 | 0.002 |
| GO:0030005 | cellular di-, tri-valent inorganic cation homeostasis | 12 | 3.36 | 0.002 |
| GO:0002252 | immune effector process | 9 | 2.52 | 0.002 |
| GO:0042592 | homeostatic process | 26 | 7.28 | 0.002 |
| GO:0044242 | cellular lipid catabolic process | 7 | 1.96 | 0.002 |
| GO:0007610 | behavior | 18 | 5.04 | 0.003 |
| GO:0055066 | di-, tri-valent inorganic cation homeostasis | 12 | 3.36 | 0.003 |
| GO:0050878 | regulation of body fluid levels | 8 | 2.24 | 0.003 |
| GO:0006953 | acute-phase response | 5 | 1.40 | 0.003 |
| GO:0006721 | terpenoid metabolic process | 5 | 1.40 | 0.003 |
| GO:0016125 | sterol metabolic process | 7 | 1.96 | 0.003 |
| GO:0008217 | regulation of blood pressure | 8 | 2.24 | 0.004 |
| GO:0055080 | cation homeostasis | 13 | 3.64 | 0.004 |
| GO:0009062 | fatty acid catabolic process | 5 | 1.40 | 0.005 |
| GO:0030003 | cellular cation homeostasis | 12 | 3.36 | 0.005 |
| GO:0010033 | response to organic substance | 30 | 8.40 | 0.005 |
| GO:0042060 | wound healing | 10 | 2.80 | 0.006 |
| GO:0007626 | locomotory behavior | 11 | 3.08 | 0.006 |
| GO:0001775 | cell activation | 12 | 3.36 | 0.006 |
| GO:0019748 | secondary metabolic process | 7 | 1.96 | 0.007 |
| GO:0042493 | response to drug | 14 | 3.92 | 0.009 |
| GO:0045059 | positive thymic T cell selection | 3 | 0.84 | 0.009 |
| GO:0043067 | regulation of programmed cell death | 23 | 6.44 | 0.010 |
| GO:0010941 | regulation of cell death | 23 | 6.44 | 0.011 |
| GO:0002520 | immune system development | 12 | 3.36 | 0.011 |
| GO:0032101 | regulation of response to external stimulus | 9 | 2.52 | 0.011 |
| GO:0008203 | cholesterol metabolic process | 6 | 1.68 | 0.011 |
| GO:0043368 | positive T cell selection | 3 | 0.84 | 0.012 |
| GO:0006874 | cellular calcium ion homeostasis | 9 | 2.52 | 0.013 |
| GO:0048584 | positive regulation of response to stimulus | 11 | 3.08 | 0.013 |
| GO:0043933 | macromolecular complex subunit organization | 20 | 5.60 | 0.013 |
| GO:0010035 | response to inorganic substance | 12 | 3.36 | 0.013 |
| GO:0008544 | epidermis development | 7 | 1.96 | 0.013 |
| GO:0050880 | regulation of blood vessel size | 5 | 1.40 | 0.013 |
| GO:0035150 | regulation of tube size | 5 | 1.40 | 0.013 |
| GO:0030193 | regulation of blood coagulation | 4 | 1.12 | 0.014 |
| GO:0006635 | fatty acid beta-oxidation | 4 | 1.12 | 0.014 |
| GO:0006776 | vitamin A metabolic process | 4 | 1.12 | 0.014 |
| GO:0055074 | calcium ion homeostasis | 9 | 2.52 | 0.014 |
| GO:0001558 | regulation of cell growth | 9 | 2.52 | 0.015 |
| GO:0045861 | negative regulation of proteolysis | 4 | 1.12 | 0.015 |
| GO:0003018 | vascular process in circulatory system | 5 | 1.40 | 0.015 |
| GO:0042311 | vasodilation | 4 | 1.12 | 0.017 |
| GO:0030855 | epithelial cell differentiation | 7 | 1.96 | 0.017 |
| GO:0042981 | regulation of apoptosis | 22 | 6.16 | 0.017 |
| GO:0060429 | epithelium development | 11 | 3.08 | 0.017 |
| GO:0030162 | regulation of proteolysis | 5 | 1.40 | 0.018 |
| GO:0001523 | retinoid metabolic process | 4 | 1.12 | 0.018 |
| GO:0016101 | diterpenoid metabolic process | 4 | 1.12 | 0.018 |
| GO:0031214 | biomineral formation | 4 | 1.12 | 0.018 |
| GO:0010038 | response to metal ion | 9 | 2.52 | 0.019 |
| GO:0007398 | ectoderm development | 7 | 1.96 | 0.019 |
| GO:0006875 | cellular metal ion homeostasis | 9 | 2.52 | 0.020 |
| GO:0032844 | regulation of homeostatic process | 7 | 1.96 | 0.020 |
| GO:0006935 | chemotaxis | 6 | 1.68 | 0.020 |
| GO:0042330 | taxis | 6 | 1.68 | 0.020 |
| GO:0048534 | hemopoietic or lymphoid organ development | 11 | 3.08 | 0.020 |
| GO:0015671 | oxygen transport | 3 | 0.84 | 0.021 |
| GO:0050818 | regulation of coagulation | 4 | 1.12 | 0.022 |
| GO:0010959 | regulation of metal ion transport | 6 | 1.68 | 0.022 |
| GO:0048545 | response to steroid hormone stimulus | 12 | 3.36 | 0.022 |
| GO:0043068 | positive regulation of programmed cell death | 13 | 3.64 | 0.024 |
| GO:0006720 | isoprenoid metabolic process | 5 | 1.40 | 0.024 |
| GO:0055065 | metal ion homeostasis | 9 | 2.52 | 0.024 |
| GO:0010942 | positive regulation of cell death | 13 | 3.64 | 0.025 |
| GO:0045582 | positive regulation of T cell differentiation | 4 | 1.12 | 0.026 |
| GO:0040008 | regulation of growth | 12 | 3.36 | 0.026 |
| GO:0002253 | activation of immune response | 6 | 1.68 | 0.028 |
| GO:0045061 | thymic T cell selection | 3 | 0.84 | 0.028 |
| GO:0009991 | response to extracellular stimulus | 12 | 3.36 | 0.028 |
| GO:0008629 | induction of apoptosis by intracellular signals | 4 | 1.12 | 0.030 |
| GO:0045621 | positive regulation of lymphocyte differentiation | 4 | 1.12 | 0.030 |
| GO:0051241 | negative regulation of multicellular organismal process | 8 | 2.24 | 0.030 |
| GO:0051085 | chaperone mediated protein folding requiring cofactor | 3 | 0.84 | 0.032 |
| GO:0009725 | response to hormone stimulus | 17 | 4.76 | 0.032 |
| GO:0032846 | positive regulation of homeostatic process | 4 | 1.12 | 0.032 |
| GO:0042573 | retinoic acid metabolic process | 3 | 0.84 | 0.036 |
| GO:0030195 | negative regulation of blood coagulation | 3 | 0.84 | 0.036 |
| GO:0009636 | response to toxin | 5 | 1.40 | 0.036 |
| GO:0051924 | regulation of calcium ion transport | 5 | 1.40 | 0.036 |
| GO:0043269 | regulation of ion transport | 6 | 1.68 | 0.036 |
| GO:0048145 | regulation of fibroblast proliferation | 4 | 1.12 | 0.037 |
| GO:0001869 | negative regulation of complement activation, lectin pathway | 2 | 0.56 | 0.037 |
| GO:0001868 | regulation of complement activation, lectin pathway | 2 | 0.56 | 0.037 |
| GO:0010890 | positive regulation of sequestering of triglyceride | 2 | 0.56 | 0.037 |
| GO:0016485 | protein processing | 6 | 1.68 | 0.039 |
| GO:0022411 | cellular component disassembly | 4 | 1.12 | 0.039 |
| GO:0006692 | prostanoid metabolic process | 3 | 0.84 | 0.040 |
| GO:0006693 | prostaglandin metabolic process | 3 | 0.84 | 0.040 |
| GO:0022405 | hair cycle process | 4 | 1.12 | 0.042 |
| GO:0022404 | molting cycle process | 4 | 1.12 | 0.042 |
| GO:0034440 | lipid oxidation | 4 | 1.12 | 0.042 |
| GO:0019395 | fatty acid oxidation | 4 | 1.12 | 0.042 |
| GO:0001942 | hair follicle development | 4 | 1.12 | 0.042 |
| GO:0042303 | molting cycle | 4 | 1.12 | 0.044 |
| GO:0042633 | hair cycle | 4 | 1.12 | 0.044 |
| GO:0006458 | ‘de novo’ protein folding | 3 | 0.84 | 0.044 |
| GO:0045058 | T cell selection | 3 | 0.84 | 0.044 |
| GO:0009268 | response to pH | 3 | 0.84 | 0.044 |
| GO:0015669 | gas transport | 3 | 0.84 | 0.044 |
| GO:0051084 | ‘de novo’ posttranslational protein folding | 3 | 0.84 | 0.044 |
| GO:0051604 | protein maturation | 6 | 1.68 | 0.045 |
| GO:0051240 | positive regulation of multicellular organismal process | 10 | 2.80 | 0.047 |
| GO:0051605 | protein maturation by peptide bond cleavage | 5 | 1.40 | 0.047 |
| GO:0043065 | positive regulation of apoptosis | 12 | 3.36 | 0.049 |
| GO:0050819 | negative regulation of coagulation | 3 | 0.84 | 0.049 |
| GO:0045597 | positive regulation of cell differentiation | 10 | 2.80 | 0.050 |
| Table 3. B | ||||
| B: FHH.Pkhd1 misregulated biological processes | ||||
| GO:0006700 | C21-steroid hormone biosynthetic process | 3 | 1.71 | 0.001 |
| GO:0048864 | stem cell development | 4 | 2.29 | 0.002 |
| GO:0045449 | regulation of transcription | 27 | 15.43 | 0.002 |
| GO:0034754 | cellular hormone metabolic process | 5 | 2.86 | 0.003 |
| GO:0006397 | mRNA processing | 8 | 4.57 | 0.003 |
| GO:0042445 | hormone metabolic process | 6 | 3.43 | 0.003 |
| GO:0048863 | stem cell differentiation | 4 | 2.29 | 0.004 |
| GO:0001568 | blood vessel development | 8 | 4.57 | 0.005 |
| GO:0008207 | C21-steroid hormone metabolic process | 3 | 1.71 | 0.005 |
| GO:0001944 | vasculature development | 8 | 4.57 | 0.006 |
| GO:0016071 | mRNA metabolic process | 8 | 4.57 | 0.007 |
| GO:0007617 | mating behavior | 3 | 1.71 | 0.007 |
| GO:0016055 | Wnt receptor signaling pathway | 5 | 2.86 | 0.007 |
| GO:0010817 | regulation of hormone levels | 6 | 3.43 | 0.014 |
| GO:0019098 | reproductive behavior | 3 | 1.71 | 0.015 |
| GO:0006396 | RNA processing | 9 | 5.14 | 0.017 |
| GO:0007618 | mating | 3 | 1.71 | 0.021 |
| GO:0008380 | RNA splicing | 6 | 3.43 | 0.024 |
| GO:0019827 | stem cell maintenance | 3 | 1.71 | 0.025 |
| GO:0000377 | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 5 | 2.86 | 0.025 |
| GO:0000375 | RNA splicing, via transesterification reactions | 5 | 2.86 | 0.025 |
| GO:0000398 | nuclear mRNA splicing, via spliceosome | 5 | 2.86 | 0.025 |
| GO:0048514 | blood vessel morphogenesis | 6 | 3.43 | 0.027 |
| GO:0042446 | hormone biosynthetic process | 3 | 1.71 | 0.028 |
| GO:0006694 | steroid biosynthetic process | 4 | 2.29 | 0.030 |
| GO:0051705 | behavioral interaction between organisms | 3 | 1.71 | 0.034 |
| GO:0032528 | microvillus organization | 2 | 1.14 | 0.036 |
| GO:0030033 | microvillus assembly | 2 | 1.14 | 0.036 |
| GO:0045777 | positive regulation of blood pressure | 3 | 1.71 | 0.036 |
| GO:0043062 | extracellular structure organization | 5 | 2.86 | 0.037 |
| GO:0043627 | response to estrogen stimulus | 5 | 2.86 | 0.046 |
| GO:0030030 | cell projection organization | 8 | 4.57 | 0.046 |
| GO:0048545 | response to steroid hormone stimulus | 7 | 4.00 | 0.050 |
A: genes up- or downregulated in PCK (>1.45 or < −1.45-fold) and not differentially expressed (<1.2 or > −1.2), or expressed in the opposite direction in FHH.Pkhd1 were considered “uniquely misregulated” in PCK and uploaded into to identify enriched biological processes (BP) to generate part A. B: genes up- or downregulated in FHH.Pkhd1(>1.45 of <−1.45-fold) and not differentially expressed (<1.2 or > −1.2), or expressed in the opposite direction in PCK were considered “uniquely misregulated” in FHH.Pkhd1 and uploaded into DAVID to identify enriched biological processes for part B. Gene ontology (GO) identifiers are listed in the lefthand column. Count indicates the number of molecules from the gene list in each BP, % is the percent of molecules out of the whole gene list that fell into each BP.